# R package for RIVER (RNA-Informed Variant Effect on Regulation)

## Documentation for package ‘RIVER’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

RIVER-package | RIVER: R package for an implementation of an extensible predictive model for combining whole genome sequences with molecular phenotypes to identify high-impact rare variants.
appRIVER | Application of RIVER
evaRIVER | Evaluation of RIVER
getData | Get coordinated data from a compressed file for RIVER
getFuncRvFeat | Posterior probabilities of FR given G
getFuncRvPosteriors | Posterior probabilities of FR given G and E.
integratedEM | An iterative expectation-maximization algorithm for RIVER
mleBeta | Maximum likelihoood estimate of beta.
mleTheta | Maximum likelihoood estimate of theta.
plotPosteriors | Draw scatter plots of posterior probabilities from both RIVER GAM in terms of outlier status.
RIVER | RIVER: R package for an implementation of an extensible predictive model for combining whole genome sequences with molecular phenotypes to identify high-impact rare variants.
testPosteriors | Test posterior probabilities of FR given G and E